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              grep rough audit - static analysis tool
                  v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
sspace-2.1.1+dfsg/SSPACE_Basic.pl-223-#-------------------------------------------------READING AND CONVERTING INPUT SEQUENCES
sspace-2.1.1+dfsg/SSPACE_Basic.pl:224:  system("perl $Bin/bin/readLibFiles.pl $libraryfile $base_name $extending $unpaired $min_overlap $threads");
sspace-2.1.1+dfsg/SSPACE_Basic.pl-225-  checkStatus();
sspace-2.1.1+dfsg/SSPACE_Basic.pl-226-#-------------------------------------------------FORMATTING OR EXTENDING CONTIGS
sspace-2.1.1+dfsg/SSPACE_Basic.pl:227:  system("perl $Bin/bin/ExtendOrFormatContigs.pl $contig $base_name $extending $filecontig $MIN_READ_LENGTH $base_overlap $min_overlap $min_base_ratio $max_trim $verbose $Bin $minContigLength $libraryfile $gaps $threads");
sspace-2.1.1+dfsg/SSPACE_Basic.pl-228-  checkStatus();
##############################################
sspace-2.1.1+dfsg/SSPACE_Basic.pl-283-#-------------------------------------------------Scaffold the contigs and generate .scaffold file
sspace-2.1.1+dfsg/SSPACE_Basic.pl:284:    system("perl $Bin/bin/PairingAndScaffolding.pl $Bin $gaps $contig $base_name $issues $distribution $verbose $lib $insert_size $min_allowed $scaffold $min_links $max_link_ratio $orientation $threads") if(!$tabfile);
sspace-2.1.1+dfsg/SSPACE_Basic.pl:285:    system("perl $Bin/bin/PairingAndScaffolding.pl $Bin $gaps $contig $base_name $issues $distribution $verbose $lib $insert_size $min_allowed $scaffold $min_links $max_link_ratio $orientation $threads $tabfile $fileB $filecontig $evidencefile") if($tabfile);
sspace-2.1.1+dfsg/SSPACE_Basic.pl-286-    checkStatus();
##############################################
sspace-2.1.1+dfsg/SSPACE_Basic_v2.0.pl-223-#-------------------------------------------------READING AND CONVERTING INPUT SEQUENCES
sspace-2.1.1+dfsg/SSPACE_Basic_v2.0.pl:224:  system("perl $Bin/bin/readLibFiles.pl $libraryfile $base_name $extending $unpaired $min_overlap $threads");
sspace-2.1.1+dfsg/SSPACE_Basic_v2.0.pl-225-  checkStatus();
sspace-2.1.1+dfsg/SSPACE_Basic_v2.0.pl-226-#-------------------------------------------------FORMATTING OR EXTENDING CONTIGS
sspace-2.1.1+dfsg/SSPACE_Basic_v2.0.pl:227:  system("perl $Bin/bin/ExtendOrFormatContigs.pl $contig $base_name $extending $filecontig $MIN_READ_LENGTH $base_overlap $min_overlap $min_base_ratio $max_trim $verbose $Bin $minContigLength $libraryfile $gaps $threads");
sspace-2.1.1+dfsg/SSPACE_Basic_v2.0.pl-228-  checkStatus();
##############################################
sspace-2.1.1+dfsg/SSPACE_Basic_v2.0.pl-283-#-------------------------------------------------Scaffold the contigs and generate .scaffold file
sspace-2.1.1+dfsg/SSPACE_Basic_v2.0.pl:284:    system("perl $Bin/bin/PairingAndScaffolding.pl $Bin $gaps $contig $base_name $issues $distribution $verbose $lib $insert_size $min_allowed $scaffold $min_links $max_link_ratio $orientation $threads") if(!$tabfile);
sspace-2.1.1+dfsg/SSPACE_Basic_v2.0.pl:285:    system("perl $Bin/bin/PairingAndScaffolding.pl $Bin $gaps $contig $base_name $issues $distribution $verbose $lib $insert_size $min_allowed $scaffold $min_links $max_link_ratio $orientation $threads $tabfile $fileB $filecontig $evidencefile") if($tabfile);
sspace-2.1.1+dfsg/SSPACE_Basic_v2.0.pl-286-    checkStatus();
##############################################
sspace-2.1.1+dfsg/bin/ExtendOrFormatContigs.pl-341-  &printMessage("\n=>".getDate().": Building Bowtie index for contigs\n");
sspace-2.1.1+dfsg/bin/ExtendOrFormatContigs.pl:342:  system("bowtie-build $contigFile bowtieoutput/$bowtieout --quiet --noref") == 0 || die "\nBowtie-build error; $?"; # returns exit status values
sspace-2.1.1+dfsg/bin/ExtendOrFormatContigs.pl-343-  &printMessage("\n=>".getDate().": Mapping reads to Bowtie index\n");
##############################################
sspace-2.1.1+dfsg/bin/PairingAndScaffolding.pl-823-   &printMessage("\n=>".getDate().": Building Bowtie index for contigs\n");
sspace-2.1.1+dfsg/bin/PairingAndScaffolding.pl:824:   system("bowtie-build $contigFile bowtieoutput/$bowtieout --quiet --noref") == 0 || die "\nBowtie-build error; $?"; # returns exit status values
sspace-2.1.1+dfsg/bin/PairingAndScaffolding.pl-825-   
##############################################
sspace-2.1.1+dfsg/tools/estimate_insert_size.pl-104-  my $bowtieout = "contig$fname.bowtieIndex";
sspace-2.1.1+dfsg/tools/estimate_insert_size.pl:105:  system("bowtie-build $contig bowtieoutput/$bowtieout --quiet --noref") == 0 || die "\nBowtie-build error; $?"; # returns exit status values
sspace-2.1.1+dfsg/tools/estimate_insert_size.pl-106-
##############################################
sspace-2.1.1+dfsg/tools/fq_all2std.pl-143-  my $arg = shift;
sspace-2.1.1+dfsg/tools/fq_all2std.pl:144:  system("$Bin/srf-conversions/illumina2srf $arg");
sspace-2.1.1+dfsg/tools/fq_all2std.pl-145-}
##############################################
sspace-2.1.1+dfsg/tools/fq_all2std.pl-160-  my $arg = shift;
sspace-2.1.1+dfsg/tools/fq_all2std.pl:161:  system("$Bin/srf-conversions/illumina2srf -b $arg");
sspace-2.1.1+dfsg/tools/fq_all2std.pl-162-}
##############################################
sspace-2.1.1+dfsg/.pc/shebangs.patch/bin/ExtendOrFormatContigs.pl-340-  &printMessage("\n=>".getDate().": Building Bowtie index for contigs\n");
sspace-2.1.1+dfsg/.pc/shebangs.patch/bin/ExtendOrFormatContigs.pl:341:  system("bowtie-build $contigFile bowtieoutput/$bowtieout --quiet --noref") == 0 || die "\nBowtie-build error; $?"; # returns exit status values
sspace-2.1.1+dfsg/.pc/shebangs.patch/bin/ExtendOrFormatContigs.pl-342-  &printMessage("\n=>".getDate().": Mapping reads to Bowtie index\n");
##############################################
sspace-2.1.1+dfsg/.pc/shebangs.patch/bin/PairingAndScaffolding.pl-822-   &printMessage("\n=>".getDate().": Building Bowtie index for contigs\n");
sspace-2.1.1+dfsg/.pc/shebangs.patch/bin/PairingAndScaffolding.pl:823:   system("bowtie-build $contigFile bowtieoutput/$bowtieout --quiet --noref") == 0 || die "\nBowtie-build error; $?"; # returns exit status values
sspace-2.1.1+dfsg/.pc/shebangs.patch/bin/PairingAndScaffolding.pl-824-   
##############################################
sspace-2.1.1+dfsg/.pc/shebangs.patch/tools/estimate_insert_size.pl-103-  my $bowtieout = "contig$fname.bowtieIndex";
sspace-2.1.1+dfsg/.pc/shebangs.patch/tools/estimate_insert_size.pl:104:  system("bowtie-build $contig bowtieoutput/$bowtieout --quiet --noref") == 0 || die "\nBowtie-build error; $?"; # returns exit status values
sspace-2.1.1+dfsg/.pc/shebangs.patch/tools/estimate_insert_size.pl-105-
##############################################
sspace-2.1.1+dfsg/.pc/shebangs.patch/tools/fq_all2std.pl-143-  my $arg = shift;
sspace-2.1.1+dfsg/.pc/shebangs.patch/tools/fq_all2std.pl:144:  system("$Bin/srf-conversions/illumina2srf $arg");
sspace-2.1.1+dfsg/.pc/shebangs.patch/tools/fq_all2std.pl-145-}
##############################################
sspace-2.1.1+dfsg/.pc/shebangs.patch/tools/fq_all2std.pl-160-  my $arg = shift;
sspace-2.1.1+dfsg/.pc/shebangs.patch/tools/fq_all2std.pl:161:  system("$Bin/srf-conversions/illumina2srf -b $arg");
sspace-2.1.1+dfsg/.pc/shebangs.patch/tools/fq_all2std.pl-162-}